Abstract The advent of DNA origami technology greatly simplified the design and construction of nanometer‐sized DNA objects. The self‐assembly of a DNA‐origami structure is a straightforward process in which a long single‐stranded scaffold (often from the phage M13mp18) is folded into basically any desired shape with the help of a multitude of short helper strands. This approach enables the ready generation of objects with an addressable surface area of a few thousand nm 2 and with a single “pixel” resolution of about 6 nm. The process is rapid, puts low demands on experimental conditions, and delivers target products in high yields. These features make DNA origami the method of choice in structural DNA nanotechnology when two‐ and three‐dimensional objects are desired. This Minireview summarizes recent advances in the design of DNA origami nanostructures, which open the door to numerous exciting applications.
Synthetic DNA filaments exploit the programmability of the individual units and their predictable self-association to mimic the structural and dynamic features of natural protein filaments. Among them, DNA origami filamentous structures are of particular interest, due to the versatility of morphologies, mechanical properties, and functionalities attainable. We here explore the thermodynamic and kinetic properties of linear structures grown from a ditopic DNA origami unit, i.e., a monomer with two distinct interfaces, and employ either base-hybridization or base-stacking interactions to trigger the dimerization and polymerization process. By observing the temporal evolution of the system toward equilibrium, we reveal kinetic aspects of filament growth that cannot be easily captured by postassembly studies. Our work thus provides insights into the thermodynamics and kinetics of hierarchical DNA origami assembly and shows how it can be mastered by the anisotropy of the building unit and its self-association mode.
If the face fits: Self-labeling fusion proteins have been used for the site-specific decoration of DNA origami. This method even allows individual faces of the quasi-two-dimensional plane of the nanostructure to be specifically decorated (see picture), thereby enabling directional immobilization and thus control over the accessibility of distinct proteins presented on the structure. Detailed facts of importance to specialist readers are published as "Supporting Information". Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Abstract Within the cell, chemical reactions are often confined and organized through a modular architecture. This facilitates the targeted localization of molecular species and their efficient translocation to subsequent sites. Here, we present a cell-free nanoscale model that exploits this compartmentalization principle to carry out regulated protein unfolding and degradation. Our model is composed of two connected DNA origami nanocompartments, one containing the protein unfolding machine, p97, and the other housing the protease chymotrypsin. We achieve the unidirectional immobilization of p97, establishing a ‘gateway’ mechanism that controls compartment accessibility and directionality of substrate processing. Our data show that, whereas spatial confinement increases the reaction rate of each individual enzyme, their physical connection into a chimera further improves their performance, minimizing off-target proteolysis. We anticipate that our modular approach may serve as a blueprint for reshaping biocatalytic pathways and stimulating the creation of nanofactories with capabilities beyond those observed in natural systems.
Verzweigte DNA: Fortschritte beim Aufbau dendritischer DNA-Strukturen ermöglichen Anwendungen zum Nachweis von Pathogenen sowie die Herstellung von Plättchen aus DNA-Hydrogel-Biomaterialien (links im Schema), die als Matrize für die Proteinproduktion in einem Zellextrakt fungieren, der RNA-Polymerase (rot), Ribosomen (gelb) und andere Komponenten enthält (rechts).
RNA-binding proteins (RBPs) are essential regulators controlling both the cellular transcriptome and translatome. These processes enable cellular plasticity, an important prerequisite for growth. Cellular growth is a complex, tightly controlled process. Using cancer cells as model, we looked for RBPs displaying strong expression in published transcriptome datasets. Interestingly, we found the Pumilio (Pum) protein family to be highly expressed in all these cells. Moreover, we observed that Pum2 is regulated by basic fibroblast growth factor (bFGF). bFGF selectively enhances protein levels of Pum2 and the eukaryotic initiation factor 4E (eIF4E). Exploiting atomic force microscopy and in vitro pulldown assays, we show that Pum2 selects for eIF4E mRNA binding. Loss of Pum2 reduces eIF4E translation. Accordingly, depletion of Pum2 led to decreased soma size and dendritic branching of mature neurons, which was accompanied by a reduction in essential growth factors. In conclusion, we identify Pum2 as an important growth factor for mature neurons. Consequently, it is tempting to speculate that Pum2 may promote cancer growth.
